Variant report

Variant	rs11738
Chromosome Location	chr12:51581007-51581008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51474666..51478844-chr12:51578009..51583588,6	MCF-7	breast:
2	chr12:51580860..51582633-chr17:57922811..57925538,2	MCF-7	breast:
3	chr12:51579329..51581068-chr12:51630464..51632697,2	K562	blood:
4	chr12:51440541..51442704-chr12:51579931..51581494,2	MCF-7	breast:
5	chr12:51565656..51568783-chr12:51579080..51582144,3	K562	blood:
6	chr12:51570670..51572206-chr12:51580870..51582491,2	K562	blood:

Variant related genes	Relation type
ENSG00000183283	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1056897	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169726	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169727	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169729	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169731	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11169732	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169736	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169742	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169752	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169754	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11833022	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs12809832	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12810455	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12810596	0.80[AMR][1000 genomes]
rs12810700	0.84[AMR][1000 genomes]
rs12811508	0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12811684	0.84[GIH][hapmap];0.92[MEX][hapmap]
rs12814498	0.84[AMR][1000 genomes]
rs12819225	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12819517	0.88[AMR][1000 genomes]
rs12820559	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12823402	0.81[AMR][1000 genomes]
rs12826153	0.84[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs12829630	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12833565	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17296192	0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34057357	0.81[AMR][1000 genomes]
rs34481246	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34498074	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768967	0.84[GIH][hapmap]
rs6580784	0.84[GIH][hapmap];0.92[MEX][hapmap]
rs6580792	0.83[CHB][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6580793	0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67293043	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7954140	0.84[GIH][hapmap];0.84[MEX][hapmap]
rs7958064	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7960381	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7964570	0.84[AMR][1000 genomes]
rs7976777	0.80[AMR][1000 genomes]
rs7977104	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7978723	0.81[GIH][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11738	TFCP2	cis	cerebellum	SCAN
rs11738	TMPRSS12	cis	parietal	SCAN
rs11738	CSRNP2	cis	cerebellum	SCAN
rs11738	COL2A1	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51567400-51583400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51567400-51584000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:51567400-51610600	Weak transcription	Right Atrium	heart
4	chr12:51574800-51583400	Weak transcription	Aorta	Aorta
5	chr12:51575600-51583600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51575800-51583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:51577600-51582400	Weak transcription	Brain Substantia Nigra	brain
8	chr12:51577600-51583000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:51577800-51582000	Weak transcription	Brain Anterior Caudate	brain
10	chr12:51577800-51583400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:51578000-51582200	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:51578000-51583000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:51578000-51583400	Weak transcription	Left Ventricle	heart
14	chr12:51578000-51583400	Weak transcription	Ovary	ovary
15	chr12:51578000-51583600	Weak transcription	Pancreas	Pancrea
16	chr12:51578000-51587600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:51578200-51582200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:51578200-51582200	Weak transcription	Brain Germinal Matrix	brain
19	chr12:51578200-51586000	Weak transcription	Fetal Heart	heart
20	chr12:51578200-51596800	Weak transcription	Fetal Lung	lung
21	chr12:51578400-51583800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:51579000-51583000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:51579400-51581600	Weak transcription	Fetal Brain Female	brain
24	chr12:51579600-51583600	Enhancers	Fetal Thymus	thymus
25	chr12:51580000-51581200	Enhancers	GM12878-XiMat	blood
26	chr12:51580000-51581400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:51580000-51581600	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:51580000-51581600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:51580200-51581400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:51580200-51581400	Enhancers	Spleen	Spleen
31	chr12:51580200-51581600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr12:51580200-51581800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:51580200-51582200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:51580200-51582200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:51580200-51582200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:51580200-51582600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:51580200-51583200	Enhancers	Primary B cells from peripheral blood	blood
38	chr12:51580200-51583400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:51580200-51583400	Weak transcription	Right Ventricle	heart
40	chr12:51580400-51581200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:51580400-51581200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:51580400-51581400	Enhancers	Psoas Muscle	Psoas
43	chr12:51580400-51583400	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:51580400-51583600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:51580400-51592000	Weak transcription	Gastric	stomach
46	chr12:51580600-51581800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:51580600-51581800	Enhancers	Fetal Stomach	stomach
48	chr12:51580600-51582200	Bivalent Enhancer	HepG2	liver
49	chr12:51580600-51583400	Weak transcription	Fetal Intestine Small	intestine
50	chr12:51580600-51583800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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